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BioC 3.5: CHECK report for RITAN on veracruz2

This page was generated on 2017-10-18 14:35:40 -0400 (Wed, 18 Oct 2017).

Package 1119/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RITAN 1.0.0
Michael Zimmermann
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/RITAN
Branch: RELEASE_3_5
Last Commit: 9c887cb
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RITAN
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RITAN_1.0.0.tar.gz
StartedAt: 2017-10-18 08:21:00 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 08:22:41 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 100.7 seconds
RetCode: 0
Status:  OK 
CheckDir: RITAN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RITAN_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RITAN.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RITAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RITAN’ version ‘1.0.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RITAN’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
check_any_net_input: no visible binding for global variable
  ‘network_list’
enrichment_symbols: no visible binding for global variable
  ‘active_genesets’
enrichment_symbols: no visible global function definition for ‘phyper’
enrichment_symbols: no visible global function definition for
  ‘p.adjust’
geneset.overlap: no visible global function definition for ‘hist’
icon_dual_between: no visible global function definition for
  ‘txtProgressBar’
icon_dual_between: no visible global function definition for
  ‘setTxtProgressBar’
icon_dual_between: no visible binding for global variable ‘all_symbols’
icon_dual_between: no visible binding for global variable ‘all_net’
icon_dual_between: no visible global function definition for ‘median’
icon_dual_between: no visible global function definition for ‘mad’
icon_dual_between: no visible global function definition for ‘density’
icon_dual_between: no visible global function definition for ‘plot’
icon_dual_between: no visible global function definition for ‘polygon’
icon_dual_between: no visible global function definition for ‘abline’
icon_dual_between: no visible global function definition for ‘box’
icon_single_within: no visible global function definition for
  ‘txtProgressBar’
icon_single_within: no visible global function definition for
  ‘setTxtProgressBar’
icon_single_within: no visible binding for global variable
  ‘all_symbols’
icon_single_within: no visible binding for global variable ‘all_net’
icon_single_within: no visible global function definition for ‘median’
icon_single_within: no visible global function definition for ‘mad’
icon_single_within: no visible global function definition for ‘density’
icon_single_within: no visible global function definition for ‘plot’
icon_single_within: no visible global function definition for ‘polygon’
icon_single_within: no visible global function definition for ‘abline’
icon_single_within: no visible global function definition for ‘box’
load_all_protein_coding_symbols: no visible global function definition
  for ‘read.table’
load_geneset_symbols: no visible binding for global variable
  ‘geneset_list’
load_geneset_symbols: no visible binding for global variable ‘f’
load_geneset_symbols: no visible binding for global variable
  ‘active_genesets’
network_overlap : <anonymous>: no visible binding for global variable
  ‘network_list’
network_overlap: no visible binding for global variable ‘network_list’
network_overlap : select_edges: no visible binding for global variable
  ‘network_list’
network_overlap: no visible global function definition for ‘read.table’
plot.term_enrichment_by_subset: no visible binding for global variable
  ‘Var2’
plot.term_enrichment_by_subset: no visible binding for global variable
  ‘Var1’
plot.term_enrichment_by_subset: no visible global function definition
  for ‘plot’
readGMT: no visible global function definition for ‘read.table’
readSIF: no visible global function definition for ‘read.table’
show_active_genesets_hist: no visible global function definition for
  ‘hist’
show_active_genesets_hist: no visible binding for global variable
  ‘active_genesets’
show_active_genesets_hist: no visible global function definition for
  ‘plot’
show_active_genesets_hist: no visible global function definition for
  ‘rect’
show_active_genesets_hist: no visible global function definition for
  ‘box’
ss2: no visible global function definition for ‘subSIF’
summary.term_enrichment : <anonymous>: no visible global function
  definition for ‘head’
summary.term_enrichment: no visible global function definition for
  ‘head’
summary.term_enrichment_by_subset: no visible binding for global
  variable ‘e’
summary.term_enrichment_by_subset: no visible global function
  definition for ‘head’
term.test: no visible global function definition for ‘phyper’
term_enrichment : process_source: no visible binding for global
  variable ‘active_genesets’
term_enrichment : process_source: no visible global function definition
  for ‘head’
write_simple_table: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  Var1 Var2 abline active_genesets all_net all_symbols box density e f
  geneset_list head hist mad median network_list p.adjust phyper plot
  polygon read.table rect setTxtProgressBar subSIF txtProgressBar
  write.table
Consider adding
  importFrom("graphics", "abline", "box", "hist", "plot", "polygon",
             "rect")
  importFrom("stats", "density", "mad", "median", "p.adjust", "phyper")
  importFrom("utils", "head", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
summary.term_enrichment_by_subset 1.730  0.106   7.205
term_enrichment                   0.618  0.036   6.169
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/RITAN.Rcheck/00check.log’
for details.


RITAN.Rcheck/00install.out:

* installing *source* package ‘RITAN’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RITAN)

RITAN.Rcheck/RITAN-Ex.timings:

nameusersystemelapsed
check_any_net_input1.9460.0902.099
check_net_input0.0420.0010.044
enrichment_symbols1.7160.1114.655
load_geneset_symbols0.0100.0000.012
network_overlap0.0140.0010.015
plot.term_enrichment_by_subset0.0170.0010.018
readGMT0.0010.0000.001
readSIF0.0010.0000.001
show_active_genesets_hist0.0180.0020.021
summary.term_enrichment0.8080.0493.608
summary.term_enrichment_by_subset1.7300.1067.205
term_enrichment0.6180.0366.169
term_enrichment_by_subset0.0090.0000.010
writeGMT0.0010.0000.001
write_simple_table000